We present a novel in situ mask method for the preparation of cross-sections of organic materials such as polymer multilayer films suitable for chemical imaging of buried interfaces. We demonstrate this method on a model buried interface system consisting of a piece of Scotch tape adhered to a PET substrate and a protective film used in consumer packaging. A high dose of gallium from a focused ion beam (FIB) was used to produce a damaged overlayer on the surface of the organic sample. The damaged layer has a significantly slower sputter rate compared to the native undamaged organic material. Therefore, during gas cluster ion beam (GCIB) depth profiling experiments the damaged layer functions as a mask, protecting the sample beneath and producing a cross-section at the edge of the mask. The FIB itself cannot be used directly to prepare the cross-section since the organic materials are easily damaged. A four step workflow is described including a final cleaning procedure to remove redeposited material from the cross-section. The workflow is completed in a few hours for samples up to 100 μm thickness. The method does not require sample embedding and is suited to automated analysis, which can be important benefits for industrial analysis where a variety of samples are analyzed routinely.